crocketa: an automated Snakemake framework for integrated single-cell transcriptome and immune-repertoire analysis

crocketa (single-Cell Repertoire Organization & Combined Kinetics Exploration for Transcriptomic Analysis) is an automated and adaptable Snakemake pipeline designed to perform fundamental initial stages of single-cell analysis for both transcriptomic and immune repertoire data, with additional steps for detailed assay characterization. crocketa stems from the imperative need to devise an optimal methodology for integrating and analyzing single-cell RNA sequencing (scRNA-seq) alongside single-cell T-cell Receptor (scTCR-seq) or B-Cell Receptor (scBCR-seq) data in an automated way by means of state-of-the-art tools. This pipeline encompasses basic steps from primary & secondary scRNA-seq along with the incorporation and analysis of immune repertoire, capable of accommodating both human and mouse datasets. crocketa addresses this need by providing a reproducible and automated framework for integrated analysis of single-cell transcriptomic and immune-repertoire data.